I think I mis-read your post about the sub's polarity switch. It will have nothing to do with a common ground at the input shorting out a signal, but if you do have to reverse the inputs because of the common ground then - yes- you might have to flip the polarity switch to make up for switching the polarity of the input. But in either case, the sub's polarity switch should be set to where it sounds the best.

I'd also think about driving your mains from the right-most 4 banana plugs on your sub amp, if you are not already doing so. This will put a 100 hz 6db/octave hi pass filter on your mains, keeping the very low bass out. This will substantially reduce the load on the mains and will also reduce the (usually somewhat out of phase) interaction between the sub and the mains.